Abstract
Before beginning this discussion, a brief review of immunology is required. The following is a very abbreviated overview of the paradigm as it pertains to the subject of synthetic peptides as antigens. In the vigorous field of immunology, theories of antigen presentation and cell regulation, in particular, are especially dynamic. The following discussion was accurate at the time of publication.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Berzofsky, J. A. (1985) Intrinsic and extrinsic factors in protein antigenic struc-ture. Science 229, 932–940.
Amzel, L M, Poljak, R. J., Varga, J. M., and Richards, F. F. (1974) The three dimensional structure of a combining region-ligand complex of immunoglobulin NEW at 3.5 Å resolution. Proc. Natl. Acad. Sci. USA 71, 1427–1430.
Amit, A. G., Mariuzza, R. A., Phillips, S. E. V., and Poljak, R J (1986) Three dimensional structure of an antigen-antibody complex at 2.8 Å resolution. Science 233, 747–753.
Colman, P. M., Laver, W. G., Varghese, J. N., Baker, A. T., Tulloch, P. A., Air, G M., and Webster, R. G. (1987) Three-dimensional structure of a complex of anti-body with influenza virus neuraminidase. Nature 326, 358–363
Padlan, E. A., Silverton, E. W., Sheriff, S., Cohen, G. H., Smith-Gill, S. J., and Davies, D. R. (1989) Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex. Proc. Nati Acad. Sci. USA 86, 5938–5942.
Stanfield, R. L., Fieser, T. M., Lerner, R. A., and Wilson, I. A. (1990) Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 Å. Science 248, 712–719.
Saul, A. J. and Geysen, H. M. (1990) Identification of epitopes through peptide technology, in New Generation Vaccines (Woodrow, G. C. and Levine, M. M., eds.), Dekker, New York, pp. 117–126.
Getzoff, E. D., Tainer, J. A., Lerner, R.A., and Geysen, H. M (1988) The chemis-try and mechanism of antibody binding to protein antigens. Adv. Immunol. 43, 1–98 (review)
Sheriff, S., Silverton, E. W., Padlan, E. A., and Cohen, G. H. (1987) Three-dimen-sional structure of an antigen-antibody complex. Proc. Natl. Acad. Sci. USA 84, 8075–8079.
Tainer, J. A., Deal, C. D., Geysen, H. M., Roberts, V. A., and Getzoff, E. D. (1991) Defining antibody-antigen recognition: towards engineered antibodies and epitopes. Intern. Rev. Immunol. 7, 165–188.
Hopp, T. P. and Woods, K. R. (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc. Nati. Acad. Sci. USA 78, 3824–3828.
Welling, G. W., Weijer, W. J., van der Zee, R., and Welling-Wester, S. (1985) Prediction of sequential antigenic regions in proteins. FEBS Lett. 188, 215–218.
Leszczynski, J. F. and Rose, G. D. (1986) Loops in globular proteins: a novel cat-egory of secondary structure. Science 234, 849–855.
Chou, P. Y. and Fasman, G. D. (1977) Beta-turns in proteins. J. Mol. Biol. 115, 135–175.
Gibrat, J. F., Gamier, J. O., and Robson, B. (1987) Further developments of protein secondary structure prediction using information theory J. Mol. Biol. 198, 425–443.
Ockenhouse, C F., Deal, C. D., and Carter, J M. (1991) A collagen multiple anti-gen peptide (MAP) binds CD36 and modulates CD36 specific epitope expression. Twelfth American Peptide Symposium Poster 545.
Novotny, J. and Haber, E. (1986) Static accessibility model of protein antigenicity: the case of scorpion neurotoxin. Biochemistry 25, 6748–6754.
Tainer, J. A., Getzoff, E. D., Alexander, H., Houghton, R. A, Olsen, A. J., Lerner, R. A., and Hendrickson, W. A. (1984) The reactivity of anti-peptide antibody is a function of the atomic mobility of sites in a protein. Nature 312, 127–133
Tainer, J. A., Getzoff, E. D., Paterson, Y, Olsen, A. J, and Lerner, R. A. (1985) The atomic mobility component of protein antigenicity. Ann. Rev. Immunol 3, 501–535.
Devereux, J, Haberli, P, and Smithies, O. (1984) A comprehensive set of sequence analysis programs for the VAX. Nucl Acids Res. 12, 387–401.
Palfreyman, J. W., Aitcheson, T. C, and Taylor, P. (1984) Guidelines for the pro-duction of polypeptide specific antisera using small synthetic oligopeptides as immunogens. J. Immunol. Methods. 75, 383–393.
DeLisi, C. and Berzofsky, J. A. (1985) T-cell antigenic sites tend to be amphipathic structures. Proc. Nati. Acad. Sci. USA 82, 7048–7052.
Margalit, H, Spouge, J L., Cornette, J L., Cease, K. B., DeLisi, C, and Berzofsky, J. A. (1987) Prediction of immunodominant helper T-cell antigenic sites from the primary sequence. J. Immunol. 138, 2213–2229.
Stille, C. J., Thomas, L. J., Reyes, V. L., and Humphreys, R. E. (1987) Hydropho-bic strip-of-helix algorithm for selection of T cell-presented peptides. Mol. Immunol. 24(10), 1021–1027.
Nauss, J. L., Reid, R. H., and Boedeker, E. C. (1991) Helical stability as a method of predicting peptide T-cell epitopes, in Proceedings of the Twelfth American Pep-tide Symposium, Escom B. V., Leiden, Netherlands, pp. 855,856.
Rothbard, J. B. and Taylor, W. R. (1988) A sequence pattern common to T cell epitopes. EMBO J. 7, 93–100.
Reyes, V. E., Fowlie, E. J., Lu, S., Phillips, L., Chin, L. T, Humphreys, R. E., and Lew, R. E. (1990) Comparison of three related methods to select T cell-presented sequences of protein antigens. Mol. Immunol. 27, 1021–1027.
Chou, P. Y. and Fasman, G. D. (1974) Prediction of protein conformation. Biochem. 13, 222–245.
Chou, P. Y and Fasman, G. D. (1978) Prediction of the secondary structure of proteins from their amino acid sequence. Adv. Enzymol. 47, 45–57.
Schiffer, M. and Edmundson, A. B. (1967) Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophys. J 7, 121–135.
Taylor, J. W., Miller, R J., and Kaiser, E T. (1982) Structural characterization of beta-endorphin through the design, synthesis, and study of model peptides Mol Pharamacol. 22, 657–666.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1994 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Carter, J.M. (1994). Epitope Prediction Methods. In: Dunn, B.M., Pennington, M.W. (eds) Peptide Analysis Protocols. Methods in Molecular Biology, vol 36. Humana Press. https://doi.org/10.1385/0-89603-274-4:193
Download citation
DOI: https://doi.org/10.1385/0-89603-274-4:193
Publisher Name: Humana Press
Print ISBN: 978-0-89603-274-3
Online ISBN: 978-1-59259-523-5
eBook Packages: Springer Protocols